It's possible that a formatting error has been introduced in the
env xml files. This would lead to problems in setting the env variables.
If there appear to be problems with the env variables (i.e. if the
model doesn't seem to have consistent values compared to what's set in the xml files),
then confirm that the env variables are being set properly. There are a couple
of ways to do that. First, run the ccsm_getenv script via

> cd $CASEROOT
> source ./Tools/ccsm_getenv
> env

and review the output generated by the command "env". The env variables
should match the xml settings. Another option is to edit the $CASEROOT/Tools/ccsm_getenv
script and comment out the line "rm $i:r". That should leave the shell
env files around, and they can then be reviewed. The latter approach
should be undone as soon as possible to avoid problems running ccsm_getenv
later.